sim.meta: Simulate a meta-community (and its phylogeny)

In pez: Phylogenetics for the Environmental Sciences

Simulate a meta-community (and its phylogeny)

Description

sim.meta.comm simulates species moving through a metacommunity. At each time-step each cell's next abundance for each species is env.quality - current.abundance + stochastic, and a species gets as many chances to migrate in each time-step as it has cells (the same cell could migrate multiple times). I use a Poisson for everything because I don't want half-species (these are individuals), and keeping everything in Poisson makes it easier to compare the relative rates of everything.

Usage

sim.meta.comm(
  size = 10,
  n.spp = 8,
  timesteps = 10,
  p.migrate = 0.05,
  env.lam = 10,
  abund.lam = 5,
  stoch.lam = 1
)

sim.meta.phy.comm(
  size = 10,
  n.spp = 8,
  timesteps = 10,
  p.migrate = 0.3,
  env.lam = 10,
  abund.lam = 5,
  stoch.lam = 1,
  p.speciate = 0.05
)

Arguments

size	the length and width of the meta-community in grid cells
n.spp	number of species
timesteps	number of time-steps (each discrete)
p.migrate	probability that a group of species in each grid cell will migrate to another grid cell each timestep (i.e., 10 cells occuped by a species –> 10*p.migrate chance of migration)
env.lam	lambda value for Poisson distribution used to distribute environmental quality; essentially the carrying capacity (for each species separately) for that cell
abund.lam	lambda value for Poisson distribution used to distribute initial abundances and abundance after migration
stoch.lam	lambda value for Poisson distribution of noise added to the next step abundance calculation. With equal chance, this is taken as either a positive or a negative number (see details if you're confused as to why this is Poisson!)
p.speciate	probabilty that, at each timestep, a species will speciate. A species can only speciate, migrate, or reproduce if it has individuals!

Details

sim.meta.phy.comm As above, but with a simulation of phylogeny as well - there are no additional extinction parameters, since extinction happens as a natural consequence of ecological interactions.

Value

For sim.meta.comm a list with a species-site matrix as the first slot, and the environment as the second. Rownames of the site-species are the List with the x and y co-ordinates of the simulation grid pasted together; colnames are arbitrary species names. sim.meta.comm, a comparative.comm object (since we have now simulated a phylogeny), with the same naming convention for the site names. phylogeny.

sim.meta.phy.comm comparative.comm object that describes the data; note that the rownames of the community object refer to the row.column of the data in the simulated grid assemblages.

Note

scape is a much more sophisticated simulation of the biogeography, but requires you to supply a phylogeny. You pays your money, you makes your choice.

Author(s)

Will Pearse

Will Pearse

See Also

sim.phy scape

pez documentation built on Sept. 1, 2022, 1:09 a.m.